def process_primer(self):
source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
sequences = source.sequences_for_primers(
self.form_result["primer_fwd"], self.form_result["primer_rev"], left_padding, right_padding
)
# TODO: better selective update method
c.primer_fwd = self.form_result["primer_fwd"]
c.primer_rev = self.form_result["primer_rev"]
c.left_padding = left_padding
c.right_padding = right_padding
c.sequences = sequences
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
self.__add_sequence_primer_display_attrs(
seq, primer_fwd=self.form_result["primer_fwd"], primer_rev=self.form_result["primer_rev"]
)
assayutil.set_amplicon_snps(c.sequences)
c.assay_form = h.LiteralForm(
value={"primer_fwd": self.form_result["primer_fwd"], "primer_rev": self.form_result["primer_rev"]}
)
return render("/assay/primer_output.html")
def process_location(self):
source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
sequence = source.sequence_around_loc(
self.form_result["chromosome"],
self.form_result["location"],
self.form_result["width"],
left_padding,
right_padding,
)
# TODO: better selective update method
c.chromosome = self.form_result["chromosome"]
c.location = self.form_result["location"]
c.width = self.form_result["width"]
c.left_padding = left_padding
c.right_padding = right_padding
c.sequence = sequence
c.sequences = [sequence]
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
seq.positive_display_sequence = seq.amplicon.positive_strand_sequence.lower()
seq.negative_display_sequence = seq.amplicon.negative_strand_sequence.lower()
assayutil.set_amplicon_snps(c.sequences)
c.assay_form = h.LiteralForm()
return render("/assay/location_output.html")
def process_snp(self):
snp_source = HG19Source()
seq_source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
snps = snp_source.snps_by_rsid(self.form_result["snp_rsid"])
c.assay_form = h.LiteralForm()
c.snp_rsid = self.form_result["snp_rsid"]
c.width = self.form_result["width"]
# override
if not snps or len(snps) == 0:
# TODO: figure out how to make this appear on the field error instead
session["flash"] = "Could not find a SNP with the name %s" % self.form_result["snp_rsid"]
session["flash_class"] = "error"
session.save()
return render("/assay/snp_output.html")
sequences = []
for snp in snps:
chromStart = snp["chromStart"]
chromEnd = snp["chromEnd"]
# handle insertions and single variations, normally the chromStart
# refers to the gap just before the base #
if snp["chromStart"] == snp["chromEnd"]:
chromStart = chromEnd
else:
chromStart += 1
sequence = seq_source.sequence_around_region(
snp["chrom"][3:], chromStart, chromEnd, self.form_result["width"], left_padding, right_padding
)
# sequence.snps = self._get_snps(sequence.chromosome, sequence.start, sequence.end)
sequences.append(sequence)
c.left_padding = left_padding
c.right_padding = right_padding
c.sequences = sequences
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
seq.positive_display_sequence = seq.amplicon.positive_strand_sequence.lower()
seq.negative_display_sequence = seq.amplicon.negative_strand_sequence.lower()[::-1]
assayutil.set_amplicon_snps(c.sequences)
return render("/assay/snp_output.html")
def create(self):
assay = Assay()
for k, v in self.form_result.items():
if k not in ("seq_padding_pos5", "seq_padding_pos3", "sequences"):
setattr(assay, k, v)
# avoids double lookup if lookup has already been done
if self.form_result["sequences"]:
# add 1000-padding sequence and snps to each.
seq_source = UCSCSequenceSource()
snp_source = HG19Source()
for seq in self.form_result["sequences"]:
# TODO: just call sequences_for_assay here? logic the same.
if not seq["positive_sequence"] or seq["negative_sequence"]:
sequence = seq_source.sequence(
seq["chromosome"],
seq["start_pos"] - self.form_result["seq_padding_pos5"],
seq["end_pos"] + self.form_result["seq_padding_pos3"],
)
cache_rec = HG19AssayCache(
chromosome=sequence.chromosome,
start_pos=seq["start_pos"],
end_pos=seq["end_pos"],
seq_padding_pos5=self.form_result["seq_padding_pos5"],
seq_padding_pos3=self.form_result["seq_padding_pos3"],
positive_sequence=sequence.positive_strand_sequence,
)
else:
cache_rec = HG19AssayCache(
chromosome=seq["chromosome"],
start_pos=seq["start_pos"],
end_pos=seq["end_pos"],
seq_padding_pos5=seq["padding_pos5"],
seq_padding_pos3=seq["padding_pos3"],
positive_sequence=seq["positive_sequence"] or None,
negative_sequence=seq["negative_sequence"] or None,
)
for snp in seq["snps"]:
cache_rec.snps.append(
SNP131AssayCache(
bin=snp["bin"],
chrom=snp["chrom"],
chromStart=snp["chromStart"],
chromEnd=snp["chromEnd"],
name=snp["name"],
score=snp["score"],
strand=snp["strand"],
refNCBI=snp["refNCBI"],
refUCSC=snp["refUCSC"],
observed=snp["observed"],
molType=snp["molType"],
class_=snp["class_"],
valid=snp["valid"],
avHet=snp["avHet"],
avHetSE=snp["avHetSE"],
func=snp["func"],
locType=snp["locType"],
weight=snp["weight"],
)
)
assay.cached_sequences.append(cache_rec)
Session.add(assay)
self.__update_tms(assay)
Session.commit()
redirect(url(controller="assay", action="view", id=assay.id))
